I don't think it matters, you're not going to be known as "Jack and Jill" are you?!
Yes you might get people who comment, but so what?
I have a friend named Mary, who has three sons, the eldest two of whom are named Joseph and Gabriel. When she was expecting her third child, she did have the odd individual ask her, "so if it's a boy, will this one be Jesus, or a girl Angel." They thought they were being funny (but they weren't).
I did ask her once, if she ever had concerns using the two names, and she admitted that there were occasions she reconsidered during both pregnancies (and in particular the first one, because of the Mary and Joseph thing). However she and her husband loved the names, and decided it was better to go with names they loved, rather than settle for ones they didn't.
NB: Third son was named Benjamin, just in case anyone was wondering!